U.S. Pat. Nos. 5,424,186 and 5,445,934 describe a pioneering technique for, among other things, forming and using high density arrays of molecules such as oligonucleotide, RNA, peptides, polysaccharides, and other materials. The patents are hereby incorporated by reference for all purposes. Arrays of oligonucleotides or peptides, for example, are formed on the surface by sequentially removing a photoremovable group from a surface, coupling a monomer to the exposed region of the surface, and repeating the process. These techniques have been used to form extremely dense arrays of oligonucleotides, peptides, and other materials. Such arrays are useful in, for example, drug development, gene expression monitoring, genotyping, and a variety of other applications.
The development of the nucleic acid probe array technology provides means for studying the complex regulation of expression of a large number of genes. U.S. Pat. No. 6,040,138, for example, describes the process for monitoring the expression of a large number of genes. One important aspect of gene expression regulation is the alternative splicing, a process by which different mRNAs are generated from a single gene. In some cases, the expression of a single gene can result in a large number of different mRNAs, hence, large number of different functioning proteins. For example, it has been shown that 64 different mRNA variants may be generated from a single gene. Alternative splicing is a very common regulatory mechanism. According to one estimate, at least 30% of the genes are alternatively spliced. Monitoring alternative splicing will therefore provide information for drug discovery, therapy monitoring, and diagnostics. Therefore, there is a great need in the art for methods for more efficiently determining alternatively spliced mRNA.